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get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer returns an error #4314

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KlaraDrofenik opened this issue May 25, 2023 · 3 comments · Fixed by #4316
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get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer returns an error #4314

KlaraDrofenik opened this issue May 25, 2023 · 3 comments · Fixed by #4316
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@KlaraDrofenik
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Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:08:06) [GCC 11.3.0]
CPython
Linux-5.4.0-135-generic-x86_64-with-glibc2.35
1.81

Expected behaviour

The function get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer should return the root mean square deviation of untransformed coordinates.

Actual behaviour

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[36], line 10
      8 super_imposerQPC.set_atoms([a1, a2, b1, b2], [b1, b2, a1, a2])
      9 super_imposerQPC.run()
---> 10 print(super_imposerQPC.get_init_rms())

File /opt/conda/lib/python3.10/site-packages/Bio/PDB/qcprot.py:349, in QCPSuperimposer.get_init_rms(self)
    347 if self.init_rms is None:
    348     diff = self.coords - self.reference_coords
--> 349     self.init_rms = np.sqrt(np.sum(np.dot(diff, diff), axis=0) / self._natoms)
    350 return self.init_rms

File <__array_function__ internals>:180, in dot(*args, **kwargs)

ValueError: shapes (4,3) and (4,3) not aligned: 3 (dim 1) != 4 (dim 0)

Steps to reproduce

import Bio
a1 = Bio.PDB.Atom.Atom("CA", [1, 1, 1], 0, 1, "", " CA ",1, element = "C")
a2 = Bio.PDB.Atom.Atom("CA", [2, 4, 6], 0, 1, "", " CA ",2, element = "C")
b1 = Bio.PDB.Atom.Atom("CA", [2, 2, 2], 0, 1, "", " CA ",3, element = "C")
b2 = Bio.PDB.Atom.Atom("CA", [3, 5, 7], 0, 1, "", " CA ",4, element = "C")

super_imposerQPC = Bio.PDB.qcprot.QCPSuperimposer()
super_imposerQPC.set_atoms([a1, a2, b1, b2], [b1, b2, a1, a2])
super_imposerQPC.run()
print(super_imposerQPC.get_init_rms())

Note

I think that file biopython/Bio/PDB/qcprot.py the useage of np.dot functions is problematic. I think the formula from Superimposer module, but updated for the variable names like np.sqrt(np.sum(np.sum(diff * diff)) / self.coords.shape[0]) should work.
@KlaraDrofenik KlaraDrofenik changed the title get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer returns error get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer returns an error May 25, 2023
@JoaoRodrigues
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Absolutely, thank you for catching this! Would you be willing to make a pull request or you prefer we handle it?

@JoaoRodrigues
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This should be included in #4312 if possible.

@KlaraDrofenik
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Absolutely, thank you for catching this! Would you be willing to make a pull request or you prefer we handle it?

I would prefer if you handle it.

@JoaoRodrigues JoaoRodrigues mentioned this issue May 30, 2023
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@peterjc peterjc mentioned this issue Jul 21, 2023
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Fix get_init_rms() in Bio.PDB.qcprot.QCPSuperimposer JoaoRodrigues/biopython
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@JoaoRodrigues @KlaraDrofenik